ci: switch from conda to standard python and pip

.github/workflows/ci-mf6.yml

@@ -8,7 +8,6 @@ on:
       - master
       - develop
       - 'release*'
-      - 'ci-pytest'
   pull_request:
     branches: [master, develop]
 

.github/workflows/ci.yml

@@ -8,7 +8,6 @@ on:
       - master
       - develop
       - 'release*'
-      - 'ci-pytest'
   pull_request:
     branches: [master, develop]
 
@@ -56,7 +55,6 @@ jobs:
       run:
         shell: bash
 
-    if: github.event_name != 'schedule'
     steps:
     # check out repo
     - name: Checkout flopy repo
@@ -101,7 +99,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest]
         python-version: [3.9, 3.8, 3.7]
         run-type: [std]
         test-pth: [""]
@@ -114,9 +112,17 @@ jobs:
             python-version: 3.9
             run-type: script
             test-path: run_scripts.py
+          - os: windows-latest
+            python-version: 3.9
+            run-type: std
+            test-path: ""
+          - os: windows-latest
+            python-version: 3.8
+            run-type: std
+            test-path: ""
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
 
     steps:
     # check out repo
@@ -126,35 +132,51 @@ jobs:
     - name: Get branch name
       uses: nelonoel/branch-name@v1.0.1
 
-    - name: Cache Miniconda
-      uses: actions/cache@v2.1.0
-      env:
-        # Increase this value to reset cache if environment.yml has changed
-        CACHE_NUMBER: 2
-      with:
-        path: ~/conda_pkgs_dir
-        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.run-type }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('etc/environment.yml') }}
-
-    # Standard python fails on windows without GDAL installation
-    # Using custom bash shell ("shell: bash -l {0}") with Miniconda
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2.1.1
+    - name: Setup Python
+      uses: actions/setup-python@v2.2.2
       with:
         python-version: ${{ matrix.python-version }}
-        mamba-version: "*"
-        channels: conda-forge
-        auto-update-conda: true
-        activate-environment: flopy
-        use-only-tar-bz2: true
 
-    - name: Add jupyter and jupytext to notebooks run
-      if: matrix.run-type == 'nb'
+    - name: Upgrade pip and install wheel
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel
+
+    - name: Install Python packages on Windows
+      if: runner.os == 'Windows'
       run: |
-        mamba install --name flopy jupyter jupytext
+        pip install -r etc/requirements.windows.pip.txt
 
-    - name: Add packages to flopy environment using mamba or conda
+    - name: Install Python packages on Linux and MacOS
+      if: runner.os != 'Windows'
       run: |
-        mamba env update --name flopy --file etc/environment.yml
+        pip install -r etc/requirements.full.pip.txt
+
+    - name: Download Python packages with GDAL dependencies on Windows
+      if: runner.os == 'Windows'
+      shell: python
+      run: |
+        import os
+        from gohlkegrabber import GohlkeGrabber
+        gg = GohlkeGrabber()
+        wheel_path = os.path.join(".", "wheels")
+        os.makedirs(wheel_path, exist_ok=True)
+        gg.retrieve(wheel_path, "gdal")
+        gg.retrieve(wheel_path, "rasterio")
+        gg.retrieve(wheel_path, "fiona")
+
+    - name: Install Python packages with GDAL dependencies on Windows
+      if: runner.os == 'Windows'
+      run: |
+        ls -ltr ./wheels/
+        pip install ./wheels/GDAL*
+        pip install ./wheels/rasterio*
+        pip install ./wheels/Fiona*
+
+    - name: Add jupyter and jupytext to notebooks run
+      if: matrix.run-type == 'nb'
+      run: |
+        pip install jupyter jupytext
 
     - name: Install pymake, xmipy, and flopy
       run: |
@@ -167,10 +189,16 @@ jobs:
       run: |
         pytest -v ci_prepare.py
 
-    - name: Add executables directory to path
+    - name: Add executables directory to path on Linux and MacOS
+      if: runner.os != 'Windows'
       run: |
         echo "$HOME/.local/bin" >> $GITHUB_PATH
 
+    - name: Add executables directory to path on Windows
+      if: runner.os == 'Windows'
+      run: |
+        echo "C:\Users\runneradmin\.local\bin" >> $GITHUB_PATH
+
     - name: Run pytest on autotest scripts
       if: matrix.run-type == 'std'
       working-directory: ./autotest

.github/workflows/rtd.yml

@@ -32,24 +32,22 @@ jobs:
           echo $GITHUB_REF
           echo $GITHUB_EVENT_NAME
 
-      # Standard python fails on windows without GDAL installation
-      # Using custom bash shell ("shell: bash -l {0}") with Miniconda
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.1
+      - name: Setup Python
+        uses: actions/setup-python@v2.2.2
         with:
           python-version: 3.9
-          mamba-version: "*"
-          channels: conda-forge
-          auto-update-conda: true
-          activate-environment: flopy
 
-      - name: Add jupyter and jupytext to scripts run
+      - name: Upgrade pip
+        run: |
+          python -m pip install --upgrade pip
+
+      - name: Install Python packages
         run: |
-          mamba install --name flopy jupyter jupytext
+          pip install -r etc/requirements.full.pip.txt
 
-      - name: Add packages to flopy environment
+      - name: Add jupyter and jupytext to scripts run
         run: |
-          mamba env update --name flopy --file etc/environment.yml
+          pip install jupyter jupytext
 
       - name: Install pymake, xmipy, and flopy
         run: |

etc/requirements.full.pip.txt

@@ -0,0 +1,34 @@
+matplotlib>=1.4.0
+numpy>=1.15.0
+
+# testing
+pylint
+flake8
+black
+coverage
+pytest
+pytest-xdist
+pytest-cov
+
+# optional
+appdirs
+python-dateutil>=2.4.0
+affine
+scipy
+pandas
+netcdf4
+pyshp>=2.0.0
+rasterio
+fiona
+descartes
+pyproj
+shapely
+geos
+geojson
+vtk
+
+# external dependencies
+requests
+
+# MODFLOW API dependencies
+bmipy

etc/requirements.windows.pip.txt

@@ -0,0 +1,35 @@
+matplotlib>=1.4.0
+numpy>=1.15.0
+
+# testing
+pylint
+flake8
+black
+coverage
+pytest
+pytest-xdist
+pytest-cov
+
+# optional
+appdirs
+python-dateutil>=2.4.0
+affine
+scipy
+pandas
+netcdf4
+pyshp>=2.0.0
+descartes
+pyproj
+shapely
+geos
+geojson
+vtk
+
+# external dependencies
+requests
+
+# MODFLOW API dependencies
+bmipy
+
+# golke installer
+gohlkegrabber